A study was conducted to control Rhozoctonia solani causing damping off disease in seedlings of Gossypium hirsutum with aqueous root extracts of Rubia cordifolia. In this study the R. cordifolia aqueous root extracts were also tested for sporicidal activity, shelf life period and biocontrol activity of soil mycoflora against cotton phytopathogens Rhizoctonia solani and Alternaria alternata causing damping off disease in seedlings and leaf spot diseases respectively. The results show that aqueous root extracts of R. cordifolia shows good- shelf life stability, sporicidal activity and significant biocontrol against soil mycoflora causing damping off disease in seedlings of G. hirsutum. Results of this study suggest that aqueous root extract of R. cordifolia can be used to reduce the effect of soil mycoflora on seedling of G. hirsutum.